Answer to the original question is "files". To prevent bloating (making what should be a 100mb download into a 2gb download) many things share common files, generally called "dependencies". If you look at the stock game as an example, many of the US subs use common parts from \Library\USSubParts, along with several other folders. If you look at the S-42 or the Gar, you'll find they have parent files from other subs, rather than wasting space duplicating all the shapes and textures.
Same thing applies to custom made ships, if all the files the new model is dependent on are not included in the download, then the mod that contains the files it needs has to be downloaded too. If you have a reasonable talent for hacking you can usually sort through the files from the ship model, then the files from the mod that the ship is dependent on, and package together something that will make it work without the supermod.
No offense, but if you had the knowledge to rework the ship so it could be used without the mod, you wouldn't have needed to ask the question in the first place. That doesn't mean you can't LEARN how to do that kind of thing, but it takes some serious work to get there.
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